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Introduction This scrapbook is about beneficial microbe that is Pseudomonas putida. P. putida benefits human being in bioremediation, biocontrol and organic synthesis.

Pseudomonas putida

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Images

Fluorescence microscopy image of a P. putida biofilm under flow conditions

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Colonization of alfalfa root by two strains of P. Putida

P. putida responds to signals produced by other bacteria inducing expression of theddcA gene

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ClassificationDomain: Bacteria

Phylum: Proteobacteria

Class: Gamma proteobacteria

Order: Pseudomonadales

Family: Pseudomonadaceae

Genus: Pseudomonas

Species: Pseudomonas putida

Binomial name: Pseudomonas putida

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Synonyms

Pseudomonas ovalis

Pseudomonas arvilla

Arthrobacter siderocapsulatus

Pseudomonas striata

Pseudomonas rugosa

Pseudomonas incognita

Pseudomonas convexa

Pseudomonas eisenbergii

Bacillus putidus

Bacillus fluorescens putidus

Arthrobacter siderocapsulatus

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Description

Pseudomonas putida is a long rod-shaped,gram-negative bacterium that is found in soil and freshwater environments where there is oxygen. It has one or more flagella for motility.P. putida is sensitive to the environment and will responds to temporal gradients of chemoattractant by suppressing changes in the direction of rotation of flagella.It grows optimally at 25-30 C (mesophilic)and can be easily isolated.P. putida is chemoheterotrophic.

P. putida has several strains including the KT2440, a strain that colonizes the plant roots in which there is a mutual relationship between the plant and bacteria. The surface of the root, rhizosphere, allows the bacteria to thrive from the root nutrients. In turn, the P.putida induces plant growth and protects the plants from pathogens. Because P. putida assist in promoting plant development, researchers use it in bioengineering research to develop biopesticides and to the improve plant health.

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What is Pseudomonas putida?

Ecology Pseudomonas putida are significant to the environment due to its complex metabolism and ability to control pollution. There is a high versatility of bacterial communities towards contaminations which is further increased by certain catabolic sequences on the TOL plasmids in the cell. Even the plasmids are important in sensing the environmental stress. Some of the environmental stresses are caused by benzene, xylene, and toluene, the main components of gasoline and are major sources of water contamination. P. putida can degrade the hydrocarbons of these organic solvents through oxidative reactions therefore placing P.putida as one of the most important microbes in bioremediation.

P. putida also interacts with other organisms in the soil. One such interaction with Saccharomyces cerevisiae in the rhizosphere led to beneficial effects on the state of the P. putida. Fungi S.cerevisiae produced the necessary glucose and also maintained the pH which was both favorable to the bacteria P.putida.The complex interaction of P. putida and S. cerevisiae together regulate plant health. Moreover, the bacteria itself is a great maintainer of abundant plant life. The production of the siderophores, such as pyoverdine and pyochelin, protect the plants from fungal pathogens. The mutual relationship benefits both partners. While P.putida is able to reside in the plant seed and rhizosphere, the plant is, in turn, protected from plant pathogens and able to obtain vital nutrients from the bacteria.

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Metabolism and Nutrition Pseudomonas putida is a rod-shaped, nonsporeforming, gram-negative bacteria that utilizes aerobic metabolism. P. putida is able to tolerate environmental stresses due to its diverse control of proteins including protein and peptide secretion and trafficking, protein modification and repair, protein folding and stabilization, and degradation of proteins, peptides, and glycopeptides.Some important proteins include the global regulatory proteins which link the pathway genes to the cell status.P. putida exercises a very complex metabolism, the proteins control a particular pathway that not only depends on the signal received, but also the specific promoters and regulators in the pathway. And in turn, once the signals are received, it informs the cell of the oxygen and nutrient availability. Another important protein is the Crc protein which is part of the signal transduction pathway moderating the carbon metabolism. It also functions in biofilm production.

P. putida has metabolism functions in biodegradable plastics. Styrene degradation in P. putida CA-3 degrades styrene in two pathways, that are vinyl side chain oxidation and attack on the aromatic nucleus of the molecule. P. putida also has sideospores, an iron chelating compound that allows the bacteria to enhance levels of iron and promote the active transport chain. Strains of P.putida have outer membrane receptor proteins that help transport the iron complex to the sideospores, specifically known as pyoverdines, which are found in the bacterial cell. From there the iron is used in metabolic processes where oxygen is the electron acceptor. Oxygen serves as a good electron acceptor. The oxygen byproducts, however, are toxic to the bacteria including superoxide and hydrogen peroxide. In response, P. putida produces catalase to protect the cell from the reactive properties of the byproducts.

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In addition, P. putida has important lipids that are developed as an adaptation mechanism to respond to physical and chemical stresses. The bacteria is able to change its degree of fatty acid saturation, the cyclopropane fatty acids formation, and the cis-trans isomerization. In different phases, the cell changes its characteristics to better respond to the environment. During the transition from growth to stationary phase, there is a higher degree of saturation of fatty acid and a higher membrane fluidity which improves substrate uptake, thus regulating the cell.All these characteristics allow P. putida to survive deadly toxins in the soil and allow it to thrive in contaminated areas. Its metabolism allows these bacteria to convert harmful organic solvents to nontoxic composites which are so essential to bioremediation.

In addition to the ability for P. putida to degrade synthetic compounds, it can also use an alternative metabolic pathway such as the Entner-Doudoroff pathway. In this pathway, P. putida degrades common hexoses, such as glucose and gluconate, to yield one net ATP for every glucose molecule degraded. This is in contrast to the two net ATP produced for every glucose molecule degraded in the classic glycolysis pathway.

The Entner-Doudoroff pathway begins by converting glucose to gluconate-6-phosphate through two intermediates. The first intermediate is gluconate which is then converted to 2-ketogluconate. 2-ketogluconate is then converted to gluconate-6-phosphate. It should be noted that in some cases, gluconate-6-phosphate can be produced directly via phosphorylation of gluconate. The gluconate-6-phosphate is converted to 2-Keto-3-deoxy-gluconate-6-phosphate (KDGP). Finally, KDGP is converted to triosephosphate and pyruvate. Interestingly, P. putida has many alternative pathways that it can utilize to produce energy, yet it does not use them and mainly relies on the Entner-Doudoroff pathway outlined above.

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Significants Pseudomonas putida has a very diverse aerobic metabolism that is able to degrade organic solvents such as toluene and also to convert styrene oil to biodegradable plastic Polyhydroxyalkanoates (PHA). This helps degrade the polystyrene foam which was thought to be non-biodegradable. Due to the bacteria’s strong appetite for organic pollutants, researchers are attracted to using P.putida as the “laboratory ‘workhorse’ for research on bacteria-remediated soil processes”.This bacteria is unique because it has the most genes involved in breaking down aromatic or aliphatic hydrocarbons which are hazardous chemicals caused by burning fuel, coal, tobacco, and other organic matter. There is great interest in sequencing the genome of P. putida due to its strong effect in bioremediation.

Aside from aiding in bioremediation, P. putida is very helpful in the research of different species in the genus Pseudomonas, especially Pseudomonas aeruginosa, a pathogenic bacterium that is one of the leading fatal diseases in humans. Researchers find that P. putida, although saprophytic, can aid in the research on cystic fibrosis, an inherited disorder caused by a defective CFTR chloride transporter, which leads to recurrent opportunistic infections by P.aeruginosa. The two bacteria are very closely related and share similar sequenced genomes (approximately 85% are shared), except P. putida lack the genes that determine virulence. Because of its nonpathogenic nature, many researchers find P. putida very beneficial to research due to its versatility and ease of handling.

In bioremediation,P. putida is used as a soil inoculant to remedy naphthalene contaminated soils.P. putida is capable of converting styrene oil into the biodegradable plastic PHA.This may be of use in the effective recycling of Polystyrene foam, otherwise thought

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to be non-biodegradable.

In biocontrol,P. putida has demonstrated potential biocontrol properties, as an effective antagonist of damping off diseases such as Pythium and Fusarium.

Certain variants of P. putida have been used in organic synthesis, the first example being the oxidation of benzene, employed by Prof. S. V. Ley in the synthesis of the cyclitol (+/-)pinitol.Pseudomonas putida CBB5 can live on pure caffeine and has been observed to break caffeine down into carbon dioxide and ammonia.

Chemical synthesis of indigo requires a high pH and produces waste that explodes in contact with air.However,a California biotechnology company,Genencor,has developed a method to produce indigo by using bacteria.Researchers identified a gene from P. Putida,for conversion of the bacterial by-product indole to indigo.This gene was put into Escherichia coli bacteria,which then turned blue.

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Referenceshttp://en.wikipedia.org/wiki/Pseudomonas_putida (Accessed 10/12/2013).

http://microbewiki.kenyon.edu/index.php/Pseudomonas_putida(Accessed 10/12/2013).

http://aem.asm.org/content/68/8/3795.short (Accessed 10/12/2013).

http://europepmc.org/abstract/MED/7921251/reload=0;jsessionid=KBfGVAqE0DstbiQ1E3O2.42 (Accessed 10/12/2013).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210162/ (Accessed 10/12/2013).

http://www.infoplease.com/encyclopedia/science/bacteria-beneficial-bacteria.html (Accessed 10/12/2013).

http://www.scielo.cl/scielo.php?pid=S0717-34582001000200010&script=sci_arttext (Accessed 10/12/2013).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1082534/ (Accessed 10/12/2013).

Tortora Funke Case.Microbiology An Introduction.11th edition. Pearson PLC, 2013

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My Thoughts First of all, I feel great and thankful because of having the opportunity to perform this project, that is ‘Adopt A Microbe’. I learn many things while doing this project, it really helps me a lot to broaden my knowledge.

I learn about ‘sharing is caring’. I discuss with my friend about whatever I don’t understand while doing this scrapbook. I ask for their opinion about my scrapbook. I really thank to them for helping me.

Besides, I learnt how to “explore” or search by using the internet. The internet is a good tool if we use it wisely. There are many information on the internet, which actually easy our job. In this project, I am able to compare information from various sources and know how to combine all the information into one.

Furthermore, I feel amazed for those beneficial microorganisms. They provide health benefits to humans, aiding in digestion, or even helping to prevent the establishment of colonies of pathogenic bacteria. They aid for soil enrichment with leguminous crops (nitrogen cycle) ,for preservation by pickling, for fermentation (the manufacture of alcoholic beverages, vinegar, and certain cheeses).They also assist in the decomposition of organic wastes (in septic tanks, in some sewage disposal plants, and in agriculture for soil enrichment) and toxic wastes, and for curing tobacco, retting flax, and many other specialized procedures.

The microbe that I adopt, that is Pseudomonas putida, really play many roles in the environment. This shows that beneficial bacteria not only benefits human health, but also benefits the environment. This in turn benefits our human beings.

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All in all, we must appreciate for what we have now. Everything in this world has their roles, even bacteria they also contribute to this world, so we, as a student, must do our part to contribute the this world as well.

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My Self

Name: Ho Poh LingAge: 20 years old My Highest Qualification: STPMHometown: PenangDescription about Myself: Quiet, OptimisticFavourite Thing to Do: Eating, Shopping, and SleepingFavourite Food: Penang Laksa, Penang Char Kway TeowMy Wish: Get First Class Honours

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